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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $species_info = array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ) $local_species = 'vma' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $species_info = array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ) $local_species = 'vma' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ), 'gf_id' => 'ORTHO05D001174', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ), 'data_identifier' => 'ORTHO05D001174', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D001174', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '466', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p13480' => 'bna', 'A01p39340' => 'bna', 'A01p40450' => 'bna', 'A05p35060' => 'bna', 'A05p36460' => 'bna', 'A06p00810' => 'bna', 'A07p44120' => 'bna', 'A08p01420' => 'bna', 'A08p15600' => 'bna', 'Aa31LG10G1540' => 'aar', 'Aa31LG4G2010' => 'aar', 'Aa31LG6G4280' => 'aar', 'Aa31LG8G1610' => 'aar', 'Aa31LG8G290' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3864' => 'aag', 'Actinidia21663' => 'ach', 'Actinidia21847' => 'ach', 'Actinidia21898' => 'ach', 'Actinidia39260' => 'ach', 'Ah.08g217470' => 'amhyb', 'Ah.09g234550' => 'amhyb', 'Ah.15g094810' => 'amhyb', 'AL1G62430' => 'aly', 'AL2G39430' => 'aly', 'AL3G24800' => 'aly', 'AL3G26680' => 'aly', 'AL7G31560' => 'aly', 'Aqoxy1G03467' => 'aox', 'Aqoxy7G02658' => 'aox', 'Aqoxy7G04194' => 'aox', 'arahy.Tifrunner.gnm1.ann1.195J1V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MQU6H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A7LMPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B2V5CV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W4Y87I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XK3KPA' => 'arhy', 'AT1G53730' => 'ath', 'AT1G78980' => 'ath', 'AT3G13065' => 'ath', 'AT3G14350' => 'ath', 'AT4G22130' => 'ath', 'ATR0605G228' => 'atr', 'ATR0626G114' => 'atr', 'ATR0686G163' => 'atr', 'ATR0686G176' => 'atr', 'Atru.chr1.4174' => 'acertr', 'Atru.chr10.2275' => 'acertr', 'Atru.chr3.4105' => 'acertr', 'AUR62001310' => 'cqu', 'AUR62001386' => 'cqu', 'AUR62012753' => 'cqu', 'AUR62021905' => 'cqu', 'AUR62025602' => 'cqu', 'AUR62025692' => 'cqu', 'BcaB04g17062' => 'bca', 'BcaB06g25393' => 'bca', 'BcaB06g25490' => 'bca', 'BcaB07g33305' => 'bca', 'BcaC01g00766' => 'bca', 'BcaC01g01411' => 'bca', 'BcaC05g29092' => 'bca', 'BcaC05g29214' => 'bca', 'BcaC08g43552' => 'bca', 'BcaC08g45399' => 'bca', 'BcaC09g48404' => 'bca', 'BcaC09g51159' => 'bca', 'BcaNung03761' => 'bca', 'BolC1t01582H' => 'bol', 'BolC1t04970H' => 'bol', 'BolC1t05147H' => 'bol', 'BolC3t20684H' => 'bol', 'BolC3t21496H' => 'bol', 'BolC5t33981H' => 'bol', 'BolC5t34157H' => 'bol', 'BolC6t36026H' => 'bol', 'BolC6t40303H' => 'bol', 'BraA01t01289Z' => 'bra', 'BraA01t03977Z' => 'bra', 'BraA05t22319Z' => 'bra', 'BraA05t22448Z' => 'bra', 'BraA06t23316Z' => 'bra', 'BraA07t31920Z' => 'bra', 'BraA08t32193Z' => 'bra', 'BraA08t33540Z' => 'bra', 'C01p16310' => 'bna', 'C01p50160' => 'bna', 'C01p52000' => 'bna', 'C01p52030' => 'bna', 'C03p84050' => 'bna', 'C03p91750' => 'bna', 'C05p53010' => 'bna', 'C05p54860' => 'bna', 'C06p09520' => 'bna', 'C06p52850' => 'bna', 'CAN.G1014.44' => 'can', 'CAN.G1252.2' => 'can', 'CAN.G1633.4' => 'can', 'CAN.G308.18' => 'can', 'CAN.G390.40' => 'can', 'CAN.G574.8' => 'can', 'CAN.G790.49' => 'can', 'CANSAT01G0443' => 'cansat', 'CANSAT56G2530' => 'cansat', 'CANSAT56G3607' => 'cansat', 'CARHR044040' => 'chi', 'CARHR072640' => 'chi', 'CARHR087640' => 'chi', 'CARHR089440' => 'chi', 'CARHR228960' => 'chi', 'Carub.0001s4301' => 'cru', 'Carub.0002s2584' => 'cru', 'Carub.0003s1240' => 'cru', 'Carub.0003s1405' => 'cru', 'Carub.0007s1919' => 'cru', 'Ca_00690_v3' => 'car', 'Ca_03771_v3' => 'car', 'Ca_21013_v3' => 'car', 'Ca_23468_v3' => 'car', 'CBR_g2770' => 'cbr', 'Cc04_g00110' => 'ccan', 'Cc04_g00580' => 'ccan', 'Cc09_g01270' => 'ccan', 'Cc10_g14620' => 'ccan', 'CDE04G0812' => 'cde', 'CDE05G1633' => 'cde', 'CDE05G3186' => 'cde', 'CDE06G1424' => 'cde', 'CDE06G2079' => 'cde', 'CDE07G0083' => 'cde', 'CDE07G0375' => 'cde', 'Cfa000167' => 'cfa', 'Cfa003450' => 'cfa', 'Cfa023508' => 'cfa', 'Ciclev10010883m.g' => 'ccl', 'Ciclev10014418m.g' => 'ccl', 'Ciclev10025011m.g' => 'ccl', 'Ciclev10030356m.g' => 'ccl', 'CiPaw.01G093800' => 'cil', 'CiPaw.01G210400' => 'cil', 'CiPaw.02G130100' => 'cil', 'CiPaw.09G097400' => 'cil', 'CiPaw.10G074100' => 'cil', 'ClCG01G009630' => 'cla', 'ClCG07G014220' => 'cla', 'ClCG08G004900' => 'cla', 'ClCG09G001440' => 'cla', 'COL.COLO4_19516' => 'col', 'COL.COLO4_30884' => 'col', 'COL.COLO4_31827' => 'col', 'Cpa.g.sc10.13' => 'cpa', 'Cpa.g.sc152.51' => 'cpa', 'Cpa.g.sc229.16' => 'cpa', 'CsaV3_1G046110' => 'csa', 'CsaV3_3G031130' => 'csa', 'CsaV3_6G003240' => 'csa', 'CsaV3_7G033890' => 'csa', 'CSS0003966' => 'camsi', 'CSS0005489' => 'camsi', 'CSS0010138' => 'camsi', 'CSS0035820' => 'camsi', 'DCAR_002200' => 'dca', 'DCAR_016086' => 'dca', 'DCAR_024985' => 'dca', 'Dinv20319' => 'din', 'Dinv37812' => 'din', 'Duzib160G0280' => 'dzi', 'Duzib192G0937' => 'dzi', 'Duzib235G0784' => 'dzi', 'Duzib235G1179' => 'dzi', 'ECA232G1572' => 'eca', 'ECA236G0302' => 'eca', 'ECA247G0012' => 'eca', 'EL10Ac7g18116' => 'bvu', 'EL10Ac7g18244' => 'bvu', 'EL10Ac8g20124' => 'bvu', 'Eucgr.D01360' => 'egr', 'Eucgr.J02582' => 'egr', 'Eucgr.J03194' => 'egr', 'FAN02G2311' => 'fan', 'FAN02G2943' => 'fan', 'FAN02G4469' => 'fan', 'FAN05G0888' => 'fan', 'FAN05G0893' => 'fan', 'FAN09G0099' => 'fan', 'FAN09G4028' => 'fan', 'FAN14G0721' => 'fan', 'FAN14G1844' => 'fan', 'FAN14G4072' => 'fan', 'FAN21G0433' => 'fan', 'FAN25G3172' => 'fan', 'FvH4_3g01460' => 'fve', 'FvH4_6g36180' => 'fve', 'FvH4_6g36490' => 'fve', 'Glyma.03G262700' => 'gma', 'Glyma.07G001066' => 'gma', 'Glyma.07G046800' => 'gma', 'Glyma.08G225900' => 'gma', 'Glyma.09G007200' => 'gma', 'Glyma.15G111600' => 'gma', 'Glyma.16G015400' => 'gma', 'Glyma.19G261700' => 'gma', 'Gohir.A05G116016' => 'ghi', 'Gohir.A05G142300' => 'ghi', 'Gohir.A06G113500' => 'ghi', 'Gohir.A06G142200' => 'ghi', 'Gohir.A06G150700' => 'ghi', 'Gohir.A10G011100' => 'ghi', 'Gohir.A10G049900' => 'ghi', 'Gohir.D05G116500' => 'ghi', 'Gohir.D05G144600' => 'ghi', 'Gohir.D06G117800' => 'ghi', 'Gohir.D06G148100' => 'ghi', 'Gohir.D06G156900' => 'ghi', 'Gohir.D10G010700' => 'ghi', 'Gohir.D10G050500' => 'ghi', 'Gorai.009G120500' => 'gra', 'Gorai.009G148500' => 'gra', 'Gorai.010G135500' => 'gra', 'Gorai.010G172500' => 'gra', 'Gorai.010G183400' => 'gra', 'Gorai.011G011800' => 'gra', 'Gorai.011G054100' => 'gra', 'GSVIVG01004806001' => 'vvi', 'GSVIVG01016654001' => 'vvi', 'GSVIVG01029462001' => 'vvi', 'HanXRQChr04g0094201' => 'han', 'HanXRQChr05g0129311' => 'han', 'HanXRQChr09g0277301' => 'han', 'HanXRQChr15g0470551' => 'han', 'HanXRQChr15g0497331' => 'han', 'Haze_06852' => 'cav', 'Haze_16151' => 'cav', 'Haze_16152' => 'cav', 'Haze_16225' => 'cav', 'Hma1.2p1_0090F.1_g045660' => 'hma', 'Hma1.2p1_0148F.1_g066270' => 'hma', 'Hma1.2p1_0298F.1_g117490' => 'hma', 'Hma1.2p1_0544F.1_g175490' => 'hma', 'Hma1.2p1_1104F.1_g257580' => 'hma', 'Hma1.2p1_1999F.1_g310470' => 'hma', 'HPP92_004336' => 'vpl', 'HPP92_010355' => 'vpl', 'HPP92_010491' => 'vpl', 'HPP92_021993' => 'vpl', 'HPP92_026145' => 'vpl', 'HPP92_026321' => 'vpl', 'Hund05695' => 'sun', 'Hund18555' => 'sun', 'Hund18556' => 'sun', 'Hund18626' => 'sun', 'Hund21434' => 'sun', 'Hund23438' => 'sun', 'Lalb_Chr04g0253991' => 'lal', 'Lalb_Chr04g0261281' => 'lal', 'Lalb_Chr10g0101051' => 'lal', 'Lalb_Chr15g0087741' => 'lal', 'Lalb_Chr17g0343151' => 'lal', 'Lalb_Chr18g0044831' => 'lal', 'Lalb_Chr20g0118921' => 'lal', 'Lalb_Chr25g0278521' => 'lal', 'Lj1A1235G87' => 'lonja', 'Lj1g0021092' => 'lja', 'Lj3g0000400' => 'lja', 'Lj3g0022830' => 'lja', 'Lj5A27T87' => 'lonja', 'Lj6g0005851' => 'lja', 'Lj9A539T92' => 'lonja', 'Lj9A544G36' => 'lonja', 'Lsat_1_v5_gn_0_22980' => 'lsa', 'Lsat_1_v5_gn_1_39760' => 'lsa', 'Lsat_1_v5_gn_4_89560' => 'lsa', 'Lsat_1_v5_gn_7_15161' => 'lsa', 'Manes.04G152100' => 'mes', 'Manes.06G178200' => 'mes', 'Manes.11G011300' => 'mes', 'Manes.16G003200' => 'mes', 'Manes.17G027800' => 'mes', 'Mapoly0090s0074' => 'mpo', 'MBI13_g09086_MAGBIO' => 'mbi', 'MBI13_g33569_MAGBIO' => 'mbi', 'MBI19_g45795_MAGBIO' => 'mbi', 'MD05G1351900' => 'mdo', 'MD09G1168400' => 'mdo', 'MD09G1171600' => 'mdo', 'MD10G1326000' => 'mdo', 'MD17G1155400' => 'mdo', 'MD17G1158200' => 'mdo', 'MD17G1158500' => 'mdo', 'Medtr2g024330' => 'mtr', 'Medtr4g005130' => 'mtr', 'Medtr7g117520' => 'mtr', 'Medtr8g023560' => 'mtr', 'MELO3C011517.2' => 'cme', 'MELO3C021727.2' => 'cme', 'MELO3C024302.2' => 'cme', 'MELO3C026658.2' => 'cme', 'Migut.H01588' => 'egut', 'Migut.I01144' => 'egut', 'MSTRG.10903' => 'ama', 'MSTRG.14627' => 'ama', 'MSTRG.22512' => 'ama', 'Nitab4.5_0000357g0210' => 'nta', 'Nitab4.5_0001409g0210' => 'nta', 'Nitab4.5_0002354g0100' => 'nta', 'Nitab4.5_0003757g0130' => 'nta', 'Nitab4.5_0006190g0060' => 'nta', 'Nitab4.5_0006338g0100' => 'nta', 'Nitab4.5_0006966g0070' => 'nta', 'Nitab4.5_0010570g0020' => 'nta', 'Nitab4.5_0012576g0010' => 'nta', 'Nn1g03416' => 'nnu', 'Nn1g07254' => 'nnu', 'Nn6g35750' => 'nnu', 'Nn8g41176' => 'nnu', 'Oeu006759.1' => 'oeu', 'Oeu013830.1' => 'oeu', 'Oeu038378.2' => 'oeu', 'Oeu039459.1' => 'oeu', 'Os02g0190500' => 'osa', 'Os03g0183800' => 'osa', 'Os03g0397700' => 'osa', 'Os06g0634500' => 'osa', 'Os07g0618400' => 'osa', 'Os09g0559900' => 'osa', 'Os10g0389800' => 'osa', 'Peaxi162Scf00038g02335' => 'pax', 'Peaxi162Scf00178g00216' => 'pax', 'Peaxi162Scf00207g01558' => 'pax', 'PGR004G0535' => 'pgr', 'PGR031G1943' => 'pgr', 'PGR102G1925' => 'pgr', 'PGSC0003DMG400009180' => 'stu', 'PGSC0003DMG400016709' => 'stu', 'PGSC0003DMG400028845' => 'stu', 'PGSC0003DMG402004902' => 'stu', 'Phvul.006G146100' => 'pvu', 'Phvul.009G260900' => 'pvu', 'Phvul.010G122100' => 'pvu', 'Phvul.010G165200' => 'pvu', 'Potri.001G161600' => 'ptr', 'Potri.003G073700' => 'ptr', 'Potri.004G005301' => 'ptr', 'Potri.007G002600' => 'ptr', 'Potri.011G010500' => 'ptr', 'Potri.014G001200' => 'ptr', 'Pp3c16_2580' => 'ppa', 'Pp3c23_14050' => 'ppa', 'Pp3c3_19490' => 'ppa', 'Pp3c4_12460' => 'ppa', 'Pp3c5_8240' => 'ppa', 'Pp3c6_26930' => 'ppa', 'Prupe.3G026900' => 'ppe', 'Prupe.3G030000' => 'ppe', 'Prupe.4G015700' => 'ppe', 'Psat0s3082g0040' => 'psa', 'Psat1g004040' => 'psa', 'Psat1g175520' => 'psa', 'Psat4g164560' => 'psa', 'Psat7g264760' => 'psa', 'PSO063G2034' => 'pso', 'PSO135G0001' => 'pso', 'PSO170G4071' => 'pso', 'PSO210G6440' => 'pso', 'PSO384G0092' => 'pso', 'PSO724G1397' => 'pso', 'PSO832G2605' => 'pso', 'QL05p000621' => 'qlo', 'QL05p072009' => 'qlo', 'QL05p085633' => 'qlo', 'QL05p086167' => 'qlo', 'RcHm_v2.0_Chr2g0148161' => 'rch', 'RcHm_v2.0_Chr2g0148621' => 'rch', 'RcHm_v2.0_Chr5g0002301' => 'rch', 'Rhsim02G0105000' => 'rsi', 'Rhsim08G0245900' => 'rsi', 'Rhsim08G0251800' => 'rsi', 'Sabra01G0130900' => 'sbr', 'Sabra03G0044300' => 'sbr', 'Sabra04G0002700' => 'sbr', 'Sabra07G0001900' => 'sbr', 'Sabra11G0008000' => 'sbr', 'Sabra14G0002400' => 'sbr', 'Sabra14G0002600' => 'sbr', 'SalBow6G5311' => 'sbo', 'Sc05g0009430' => 'sci', 'Sc12g0011000' => 'sci', 'Sc15g0000860' => 'sci', 'Sc15g0001180' => 'sci', 'Sed0011888' => 'sed', 'Sed0012913' => 'sed', 'Sed0021511' => 'sed', 'Sed0024112' => 'sed', 'Sed0024542' => 'sed', 'Sed0027640' => 'sed', 'SEGI_05600' => 'sgi', 'SEGI_17819' => 'sgi', 'SEGI_28560' => 'sgi', 'SEGI_30877' => 'sgi', 'SEGI_38361' => 'sgi', 'SGA_v2.0_scaffold122G33299' => 'sas', 'SGA_v2.0_scaffold49G18250' => 'sas', 'SGA_v2.0_scaffold71G23948' => 'sas', 'SGA_v2.0_scaffold89G27483' => 'sas', 'SHI25224' => 'shi', 'SHI31131' => 'shi', 'SMO200G0234' => 'smo', 'SMO203G0068' => 'smo', 'SMO364G0528' => 'smo', 'Solyc02g081070.4' => 'sly', 'Solyc03g123740.4' => 'sly', 'Solyc06g063150.4' => 'sly', 'Solyc06g063360.4' => 'sly', 'Solyc12g055720.2' => 'sly', 'Sopen02g025740' => 'spe', 'Sopen03g041510' => 'spe', 'Sopen06g022600' => 'spe', 'Sopen06g022830' => 'spe', 'Sopen12g024190' => 'spe', 'Sp1g40260' => 'spa', 'Sp3g11230' => 'spa', 'Sp3g12640' => 'spa', 'Sp5g34020' => 'spa', 'Sp7g20280' => 'spa', 'TAR383G0548' => 'tar', 'TAR383G0885' => 'tar', 'TAR383G1011' => 'tar', 'TAR624G1309' => 'tar', 'TAR626G0159' => 'tar', 'THA.LOC104810401' => 'tha', 'THA.LOC104812340' => 'tha', 'THA.LOC104812980' => 'tha', 'THA.LOC104813393' => 'tha', 'THA.LOC104815592' => 'tha', 'THA.LOC104822744' => 'tha', 'Thecc.06G052100' => 'tca', 'Thecc.06G131700' => 'tca', 'Thecc.06G227500' => 'tca', 'Thhalv10011271m.g' => 'esa', 'Thhalv10019668m.g' => 'esa', 'Thhalv10020162m.g' => 'esa', 'Thhalv10020193m.g' => 'esa', 'Thhalv10024563m.g' => 'esa', 'TPR.G12988' => 'tpr', 'TPR.G26433' => 'tpr', 'TPR.G28873' => 'tpr', 'TPR.G38749' => 'tpr', 'TWI12G1364' => 'twi', 'TWI23G0460' => 'twi', 'TWI38G1871' => 'twi', 'TWI59G1357' => 'twi', 'vmacro15803' => 'vma', 'vmacro18712' => 'vma', 'vmacro18726' => 'vma', 'VMungo0331G1220' => 'vmu', 'VMungo0331G1870' => 'vmu', 'VMungo0540G1870' => 'vmu', 'VMungo1309G1307' => 'vmu', 'Zm00001eb006270' => 'zma', 'Zm00001eb027970' => 'zma', 'Zm00001eb068080' => 'zma', 'Zm00001eb104670' => 'zma', 'Zm00001eb234920' => 'zma', 'Zm00001eb275550' => 'zma', 'Zm00001eb327580' => 'zma', 'Zm00001eb387520' => 'zma', 'Zm00001eb401630' => 'zma' ) $gf_id = 'ORTHO05D001174' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D001174' ) $data_identifier = 'ORTHO05D001174' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 4, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 2, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 7, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 1, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 4, 'twi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb401630' $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